how to install cutout animation tools
With your download in the root there is a README.md this contains install instructions:

"### Blender Addon:
Zip the coa_folder.
Go to File -> User Preferences -> Add-ons and click the “Install from file...” button.
This will install and enable the Addon for Blender. Don’t forget to save the user preferences, otherwise the addon will not be activated after restart."

as it says go inside the blender folder and zip the coa_tools folder.

then install from file and select that zip folder.